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Bookshelf: a simple curation system for the storage of biomolecular simulation data

Bookshelf: a simple curation system for the storage of biomolecular simulation data
Bookshelf: a simple curation system for the storage of biomolecular simulation data
Molecular dynamics simulations can now routinely generate data sets of several hundreds of gigabytes in size. The ability to generate this data has become easier over recent years and the rate of data production is likely to increase rapidly in the near future. One major problem associated with this vast amount of data is how to store it in a way that it can be easily retrieved at a later date. The obvious answer to this problem is a database. However, a key issue in the development and maintenance of such a database is its sustainability, which in turn depends on the ease of the deposition and retrieval process. Encouraging users to care about meta-data is difficult and thus the success of any storage system will ultimately depend on how well used by end-users the system is. In this respect we suggest that even a minimal amount of metadata if stored in a sensible fashion is useful, if only at the level of individual research groups. We discuss here, a simple database system which we call ‘Bookshelf’, that uses python in conjunction with a mysql database to provide an extremely simple system for curating and keeping track of molecular simulation data. It provides a user-friendly, scriptable solution to the common problem amongst biomolecular simulation laboratories; the storage, logging and subsequent retrieval of large numbers of simulations.
baq033
Vohra, Shabana
7348a7ff-eefc-4116-bac1-5c8c98c992d1
Hall, Benjamin A.
47044d71-5541-4097-8463-562cef47c2d3
Holdbrook, Daniel A.
d114c018-fb42-4a49-9b50-f7739feb75f5
Khalid, Syma
90fbd954-7248-4f47-9525-4d6af9636394
Biggin, Philip C.
c7394f79-450a-46c6-b77a-fadac30ded33
Vohra, Shabana
7348a7ff-eefc-4116-bac1-5c8c98c992d1
Hall, Benjamin A.
47044d71-5541-4097-8463-562cef47c2d3
Holdbrook, Daniel A.
d114c018-fb42-4a49-9b50-f7739feb75f5
Khalid, Syma
90fbd954-7248-4f47-9525-4d6af9636394
Biggin, Philip C.
c7394f79-450a-46c6-b77a-fadac30ded33

Vohra, Shabana, Hall, Benjamin A., Holdbrook, Daniel A., Khalid, Syma and Biggin, Philip C. (2010) Bookshelf: a simple curation system for the storage of biomolecular simulation data. Database, 2010, baq033. (doi:10.1093/database/baq033). (PMID:21169341)

Record type: Article

Abstract

Molecular dynamics simulations can now routinely generate data sets of several hundreds of gigabytes in size. The ability to generate this data has become easier over recent years and the rate of data production is likely to increase rapidly in the near future. One major problem associated with this vast amount of data is how to store it in a way that it can be easily retrieved at a later date. The obvious answer to this problem is a database. However, a key issue in the development and maintenance of such a database is its sustainability, which in turn depends on the ease of the deposition and retrieval process. Encouraging users to care about meta-data is difficult and thus the success of any storage system will ultimately depend on how well used by end-users the system is. In this respect we suggest that even a minimal amount of metadata if stored in a sensible fashion is useful, if only at the level of individual research groups. We discuss here, a simple database system which we call ‘Bookshelf’, that uses python in conjunction with a mysql database to provide an extremely simple system for curating and keeping track of molecular simulation data. It provides a user-friendly, scriptable solution to the common problem amongst biomolecular simulation laboratories; the storage, logging and subsequent retrieval of large numbers of simulations.

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More information

Published date: 2010

Identifiers

Local EPrints ID: 179491
URI: http://eprints.soton.ac.uk/id/eprint/179491
PURE UUID: 7fac9e2e-c677-4cb1-bafc-06256b771c8d
ORCID for Syma Khalid: ORCID iD orcid.org/0000-0002-3694-5044

Catalogue record

Date deposited: 01 Apr 2011 14:19
Last modified: 07 Oct 2020 01:54

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